rs1509729

Variant names:

• chr11-109056756-C-T
• rs1509729

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.309 in 151,954 control chromosomes in the GnomAD database, including 7,400 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46955 AN: 151836 Hom.: 7379 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 47010 AN: 151954 Hom.: 7400 Cov.: 32 AF XY: 0.313 AC XY: 23204 AN XY: 74234

African (AFR) AF: 0.327 AC: 13562 AN: 41474

American (AMR) AF: 0.333 AC: 5076 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1528 AN: 5152

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4814

European-Finnish (FIN) AF: 0.339 AC: 3579 AN: 10552

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19877 AN: 67926

Other (OTH) AF: 0.310 AC: 655 AN: 2110

Alfa AF: 0.299 Hom.: 11589

Bravo AF: 0.310

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.50
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1509729; hg19: chr11-108927483;